4kxp

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant I10D in T-state

Method: X-RAY DIFFRACTION Dmax: 87.4 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Fructose-1,6-bisphosphatase 1

Sus scrofa

UniProt P00636

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–338 Chain B; UniProt 1–338 Mutation:I10D F6P 6-O-phosphono-beta-D-fructofuranose × 4 PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 8 AMP ADENOSINE MONOPHOSPHATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.4;298 K;PEG 3350, t-butyl alcohol, 2-methyl-2,4-pentanediol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.70 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

66 other PDB entries and 79 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F16P1_PIG
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–338; UniProt 1–338 Author chain B; PDBConstruct 1–338; UniProt 1–338

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4kxp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4kxp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4kxp
Deposition date deposition_date2013-05-27
Structure title titleCrystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant I10D in T-state
Keywords keywordsAllosteric Enzymes, FBPase, T-state, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.47
Radius of gyration Rg (electron density) rg_electron25.48
Forward intensity I(0) i076976300.00
Molecular weight molecular_weight69158.0 kDa
Excluded volume excluded_volume86826 ų
Envelope volume envelope_volume99795 ų
Hydration-shell volume shell_volume32170 ų
Envelope diameter envelope_diameter92.7
Shell Rg shell_rg33.18
Envelope Rg envelope_rg25.76
Shape Rg shape_rg25.49
Total Rg total_rg26.25
Total atoms total_atoms4836
Residues n_residues620
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.4
Rg (real space) rg_real26.44
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real7.6980e+07
I(0) uncertainty (real space) i0_real_error1.1210e+06
Rg (reciprocal space) rg_reciprocal26.45
I(0) (reciprocal space) i0_reciprocal76980000.0000
Solution quality estimate total_estimate0.8876
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.399
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22370000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4kxpa_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamilye.7.1 — Carbohydrate phosphatase
Family Family familye.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like
Domain ID domain_idd4kxpb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamilye.7.1 — Carbohydrate phosphatase
Family Family familye.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (4 domains)

Domain ID domain_id4kxpA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1
Domain ID domain_id4kxpA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily80
Domain ID domain_id4kxpB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1
Domain ID domain_id4kxpB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily80

8. Citations (1)

9. Files and Curves (10)